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TP53
Final classification
VUS
TP53 c.-29+102T>G · p.?
TP53

NM_000546.6:c.-29+102T>G is an intronic variant in TP53 located at position +102 in intron 1.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.-29+102T>G
Consequence
N/A
GRCh38
chr17:7687275 A>C
GRCh37
chr17:7590593 A>C
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) + BP7 supporting (-1) = -1 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) + BP7 supporting (-1) = -1 points, which maps to VUS.
Classification rationale
PM2 BP4BP7 VUS
TP53 c.-29+102T>G

NM_000546.6:c.-29+102T>G is an intronic variant in TP53 located at position +102 in intron 1. This variant is absent from gnomAD v2.1 and v4.1 population databases, meeting PM2_Supporting per TP53 VCEP specifications (allele frequency <0.00003).1 SpliceAI predicts no impact on splicing (max delta score 0.00), meeting BP4_Supporting and BP7_Supporting per TP53 VCEP specifications (SpliceAI ≤0.1 for intronic variants).2 VCEP Tavtigian point tally: PM2_Supporting (+1), BP4_Supporting (−1), BP7_Supporting (−1) = −1, which falls in the VUS range (−1 to 5).3 Per the VCEP CAVEAT, a final point value of −1 is overridden to Likely Benign when at least two benign evidence codes are applied and PM2_Supporting is the only pathogenic code applied. With BP4_Supporting and BP7_Supporting as the two benign codes, this override applies.4 No publications identified for this variant; absent from ClinVar and COSMIC.

PM2 + BP4 + BP7 VUS
3 final_classification_framework
4 final_classification_framework
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 9 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000546.6:c.-29+102T>G is absent from both gnomAD v2.1 and v4.1, meeting the VCEP PM2_Supporting threshold of allele frequency <0.00003 (0.003%).
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)
BP4 supporting Benign
SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00, which is ≤0.1), meeting the VCEP BP4_Supporting threshold for intronic variants.
SpliceAI max delta score = 0.00no predicted splicing impactmeeting VCEP BP4_Supporting threshold of ≤0.1
BP7 supporting Benign
NM_000546.6:c.-29+102T>G is an intronic variant at position +102 (beyond +7) with SpliceAI max delta score of 0.00 (≤0.1), meeting the VCEP BP7_Supporting rule for intronic variants at or beyond +7 to -21 positions with no predicted splice impact.
Intronic variant at +102 in intron 1 (beyond +7)SpliceAI max delta score = 0.00no predicted splicing impact
Assessed · not applied
Pathogenic
PS2 No de novo data or proband information is available for this variant.
PS4 No proband prevalence data is available.
PP1 No cosegregation data is available for this variant.
PP3 VCEP PP3 for intronic variants requires SpliceAI ≥0.2.
PP4 The VCEP PP4 rule requires VAF data (5-35%) from patient observations.
Benign
BA1 VCEP BA1 requires a filtering allele frequency ≥0.001 (0.1%) in a gnomAD continental subpopulation.
BS1 VCEP BS1 requires a filtering allele frequency ≥0.0003 (0.03%) but <0.001 in a gnomAD continental subpopulation.
BS2 VCEP BS2 requires observations in older unaffected females (≥60 years without cancer).
BS4 VCEP BS4 requires lack of segregation in affected family members with LFS-associated cancers.
N/A · 13 PVS1 · PS1 · PS3 · PM1 · PM5 · PM6 · PP2 · PP5 · BS3 · BP1 · BP2 · BP5 · BP6
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC